The study of DNA analysis is playing an important role for studying genome evolution, phylogenetic and genetic analysis in recent years. Various models of genome evolution were made based on the analysis of DNA sequences, SNP, mutation, and so on. This will allows to us to incorporate extinct species into genome evolution trees. In this research, we introduce various methods to build the genome evolution tree based on extracting the core genome (e.g common genes). We built the two evolution trees based on twelve chloroplast genomes from genBank, fully annotated by: NCBI and Dogma. We made then gene quality control among the common genes in NCBI and Dogma. Comparing genes sequences from dogma with their aliases in NCBI will give to us an important role for genome evolution.  